From ebdc5c4fbda8cc0ede448fe720d5383fdab472dc Mon Sep 17 00:00:00 2001
From: Young <erin.olde@gmail.com>
Date: Fri, 15 Mar 2024 10:07:46 -0600
Subject: [PATCH] Update github_actions.config

---
 .github/workflows/github_actions.config | 71 +++++++++++--------------
 1 file changed, 31 insertions(+), 40 deletions(-)

diff --git a/.github/workflows/github_actions.config b/.github/workflows/github_actions.config
index 4e32005..31bdc24 100755
--- a/.github/workflows/github_actions.config
+++ b/.github/workflows/github_actions.config
@@ -1,33 +1,34 @@
 process {
-    maxRetries    = 0
-    maxErrors     = '-1'
+	maxRetries    = 0
+	maxErrors     = '-1'
+	
+	withLabel:process_single {
+		cpus   = { 1 }
+		memory = { 6.GB * task.attempt }
+		time   = { 10.m * task.attempt }
+	}
+	withLabel:process_low {
+		cpus   = { 2     * task.attempt }
+	        memory = { 12.GB * task.attempt }
+	        time   = { 2.h   * task.attempt }
+	}
+	withLabel:process_medium {
+		cpus   = { 2     * task.attempt }
+	        memory = { 12.GB * task.attempt }
+        	time   = { 4.h   * task.attempt }
+    	}
+    	withLabel:process_high {
+        	cpus   = { 2    * task.attempt }
+        	memory = { 12.GB * task.attempt }
+        	time   = { 16.h  * task.attempt }
+    	}
+    	withLabel:process_long {
+        	time   = { 20.h  * task.attempt }
+	}
+	withLabel:process_high_memory {
+		memory = { 12.GB * task.attempt }
+	}
 
-    withLabel:process_single {
-      cpus   = { 1 }
-      memory = { 6.GB * task.attempt }
-      time   = { 10.m * task.attempt }
-    }
-    withLabel:process_low {
-        cpus   = { 2     * task.attempt }
-        memory = { 12.GB * task.attempt }
-        time   = { 2.h   * task.attempt }
-    }
-    withLabel:process_medium {
-        cpus   = { 2     * task.attempt }
-        memory = { 12.GB * task.attempt }
-        time   = { 4.h   * task.attempt }
-    }
-    withLabel:process_high {
-        cpus   = { 2    * task.attempt }
-        memory = { 12.GB * task.attempt }
-        time   = { 16.h  * task.attempt }
-    }
-    withLabel:process_long {
-        time   = { 20.h  * task.attempt }
-    }
-    withLabel:process_high_memory {
-        memory = { 12.GB * task.attempt }
-    }
 	withName:amrfinderplus {
 		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
 	}
@@ -131,12 +132,7 @@ process {
 		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
 	}
 	withName:panaroo {
-		publishDir = { 
-			params.outdir, 
-			mode: 'link', 
-			saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
-			pattern: "panaroo/core_gene_alignment.aln"
-			}
+		publishDir = { params.outdir, mode: 'link', pattern: "panaroo/core_gene_alignment.aln"}
 		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
 	}
 	withName:pbptyper {
@@ -149,12 +145,7 @@ process {
 		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
 	}
 	withName:prokka {
-		publishDir = { 
-			params.outdir, 
-			mode: 'link', 
-			saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
-			pattern: "gff/*.gff"
-			}
+		publishDir = { params.outdir, mode: 'link', pattern: "gff/*.gff" }
 		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
 	}
 	withName:quast {